Image analysis of Arabidopsis thaliana rosettes is an important non destructive method for studying plant growth. Some work on automatic rosette measurement using image analysis has been proposed in the past, but is generally restricted to be used only in combination with specific high throughput monitoring systems. We introduce Rosette Tracker, a new open source image analysis tool for evaluation of plant shoot phenotypes. This tool is not constraint to one specific monitoring system and can be adapted to different low budget imaging set ups and requires minimal user input. In contrast to previously described monitoring tools, Rosette Tracker allows to simultaneously quantify plant growth, photosynthesis and leaf temperature related parameters through the analysis of VIS, chlorophyll fluorescence and/or thermal infra red time lapse sequences. Available for free, Rosette Tracker facilitates gaining rapid understanding of Arabidopsis thaliana genotype effects.